I use Tor hidden services to punch through NATs (mostly for SSH); it's also useful in that only you can access the service (since only you know its address), so a hidden service + random port is a cheap "port knocking" implementation.
I've also used Tor to debug firewalls. It's a good way of saying "put me in a random spot on the Internet."
Outside of that, I use Tor for whatever I can: downloading RSS feeds, instant messaging, downloading email, mostly. There's no reason not to have Tor on these things because they're all either batched or tolerant of bad latency, and it destroys a little bit of my personal information that would otherwise leak.
The onion addresses of hidden services are not themselves secret. The onion address is in fact well known, published in the directory. It's only your server's IP that a hidden service is hiding.
So please, don't treat knowledge of the onion address itself as a secret! You still have to authenticate to your service in some way.
Tor itself has a nice built-in method of authentication you can use. I don't know of a good howto, but it's documented in the man page. Search for "HiddenServiceAuthorizeClient": https://www.torproject.org/docs/tor-manual.html.en
tl;dr it's possible, and you don't have to rely on crawling the web searching for .onion addresses. You can instead become a HS directory authority, and pick your place in the DHT. Eventually you'd be able to get every address that goes into the DHT.
Latency is a problem for me. Maybe for some users, who already have very slow internet, or who live in areas with more TOR relays, it is not so noticeable, but for me the speed difference is about 10 times. Mostly not because TOR would be unbearably slow (it is not slower than regular internet 8 years ago), but because regular internet is very fast where I live.
I mean, you'll notice my strategy is to never torify anything where I'd have to actually wait for it. Except IM, which is small enough that it doesn't matter, anything I've torified is downloaded in the background anyway.
I've also used Tor to debug firewalls. It's a good way of saying "put me in a random spot on the Internet."
Outside of that, I use Tor for whatever I can: downloading RSS feeds, instant messaging, downloading email, mostly. There's no reason not to have Tor on these things because they're all either batched or tolerant of bad latency, and it destroys a little bit of my personal information that would otherwise leak.